rs9295924

Variant names:

• chr6-30814584-G-A
• rs9295924
• ENST00000399196.1:n.334C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000399196.1(LINC00243):​n.334C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 456,756 control chromosomes in the GnomAD database, including 14,388 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.18 (3128 hom., cov: 31)
  • Exomes 𝑓: 0.24 (11260 hom.)
• Consequence: LINC00243 ENST00000399196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 15 publications found

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ENSG00000293879 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00243	NR_130726.1	n.334C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000399196.1	n.334C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00243	ENST00000719489.1	n.316C>T		non_coding_transcript_exon_variant	Exon 2 of 3
LINC00243	ENST00000719491.1	n.529C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27228 AN: 151664 Hom.: 3123 Cov.: 31

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.204

GnomAD2 exomes AF: 0.272 AC: 37856 AN: 138988 AF XY: 0.274

Gnomad AFR exome AF: 0.0966

Gnomad AMR exome AF: 0.395

Gnomad ASJ exome AF: 0.330

Gnomad EAS exome AF: 0.435

Gnomad FIN exome AF: 0.173

Gnomad NFE exome AF: 0.168

Gnomad OTH exome AF: 0.234

GnomAD4 exome AF: 0.243 AC: 74002 AN: 304974 Hom.: 11260 Cov.: 0 AF XY: 0.254 AC XY: 44166 AN XY: 173592

African (AFR) AF: 0.103 AC: 885 AN: 8628

American (AMR) AF: 0.398 AC: 10855 AN: 27282

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 3539 AN: 10790

East Asian (EAS) AF: 0.424 AC: 3910 AN: 9212

South Asian (SAS) AF: 0.382 AC: 22799 AN: 59734

European-Finnish (FIN) AF: 0.169 AC: 2206 AN: 13068

Middle Eastern (MID) AF: 0.218 AC: 607 AN: 2784

European-Non Finnish (NFE) AF: 0.163 AC: 25980 AN: 159076

Other (OTH) AF: 0.224 AC: 3221 AN: 14400

GnomAD4 genome AF: 0.180 AC: 27257 AN: 151782 Hom.: 3128 Cov.: 31 AF XY: 0.188 AC XY: 13921 AN XY: 74162

African (AFR) AF: 0.0966 AC: 3996 AN: 41376

American (AMR) AF: 0.307 AC: 4670 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3472

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5158

South Asian (SAS) AF: 0.380 AC: 1830 AN: 4810

European-Finnish (FIN) AF: 0.155 AC: 1628 AN: 10502

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 11003 AN: 67924

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.170 Hom.: 3547

Bravo AF: 0.186

Asia WGS AF: 0.393 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.46
PhyloP100		0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9295924; hg19: chr6-30782361;